+Open data
-Basic information
Entry | Database: PDB / ID: 2w0r | ||||||
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Title | Crystal structure of the mutated N263D YscU C-terminal domain | ||||||
Components | YSCU | ||||||
Keywords | MEMBRANE PROTEIN / PLASMID / AUTOCLEAVAGE / RECOGNITION PROTEIN / TYPE III SECRETION SYSTEM | ||||||
Function / homology | Function and homology information | ||||||
Biological species | YERSINIA ENTEROCOLITICA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Wiesand, U. / Sorg, I. / Amstutz, M. / Wagner, S. / Van Den Heuvel, J. / Luehrs, T. / Cornelis, G.R. / Heinz, D.W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Structure of the Type III Secretion Recognition Protein Yscu from Yersinia Enterocolitica Authors: Wiesand, U. / Sorg, I. / Amstutz, M. / Wagner, S. / Van Den Heuvel, J. / Luehrs, T. / Cornelis, G.R. / Heinz, D.W. #1: Journal: J.Bacteriol. / Year: 1994 Title: Yscu, a Yersinia Enterocolitica Inner Membrane Protein Involved in Yop Secretion. Authors: Allaoui, A. / Woestyn, S. / Sluiters, C. / Cornelis, G.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w0r.cif.gz | 44.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w0r.ent.gz | 30.6 KB | Display | PDB format |
PDBx/mmJSON format | 2w0r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2w0r_validation.pdf.gz | 423.1 KB | Display | wwPDB validaton report |
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Full document | 2w0r_full_validation.pdf.gz | 425.2 KB | Display | |
Data in XML | 2w0r_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 2w0r_validation.cif.gz | 11.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w0/2w0r ftp://data.pdbj.org/pub/pdb/validation_reports/w0/2w0r | HTTPS FTP |
-Related structure data
Related structure data | 2v5gSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16851.371 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, RESIDUES 211-354 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) YERSINIA ENTEROCOLITICA (bacteria) / Strain: W22703 / Plasmid: PGEX-6-P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TUNER DE3 / References: UniProt: Q56844 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop Details: HANGING DROP METHOD USING 3 UL OF A 8 MG/ML PROTEIN SOLUTION MIXED WITH 3 UL RESERVOIR BUFFER (1.6 M (NH4)2SO4, 0.2 M NACL, 0.1 M HEPES PH 7.5) IN THE DROPLET. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.95 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 12, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→10 Å / Num. obs: 21871 / % possible obs: 96.7 % / Observed criterion σ(I): 4.8 / Redundancy: 3.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.55→1.63 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 4.8 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V5G Resolution: 1.55→10 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.354 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. MISSING RESIDUES 211-221 AND 343-354 DUE TO WEAK DENSITY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.71 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→10 Å
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Refine LS restraints |
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